Ibadats that are obligatory for Muslims like salat or fast, also have ancillary benefits. For example, fasting is said to be beneficial for our health. Judging from this, a Muslim may come to the conclusion that, whatever Allah (C.C) make us do, is beneficial for us this way or another. So, if I question about something like "This ibadat (act of worship) is a must for me, therefore I do it, but what are its benefits?", is it beneficial and encouraged, or harmful and discouraged?

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The word Islam comes from the root letters seen, laam, meem. Islam does not mean peace, but it means submission. That is, a Muslim (Arabic equivalent of "Islam-er", or one who does Islam) is someone who submits their will and desires, their actions and beliefs, everything, to almighty Allah.

This is precisely what Prophet Ibrahim said in the Qur'an:

When his Lord said to him, "Submit", he said "I have submitted [in
Islam] to the Lord of the worlds." (Surah Baqarah, verse 131)

As for the worldly benefits, or the justifications, sometimes we know it, and sometimes we don't. A famous statement of Ali ibn Abi Talib is: "If everything in Islam made logical sense, masaah (wiping over your socks instead of washing over them) would be on the bottom of the sock, not the top." Because that's where the dirt is.

Also, in da'wah, sometimes we fall into this mistake where we try to justify an action by the benefits. For example, Muslims used to say that "we don't eat pig because of the parasites, it's really unclean and bad for you." But today, pork is much more hygienic, and you can get by without getting sick. So yes, that was one benefit, but perhaps not the cause.

So ultimately, we say, Allah knows best.

As to your exact question, why would there be an issue in questioning this? Scholars have written tomes on benefits of different 'ibaadat. In fact, rasulullah (salallahu alayhi wa sallam) said in one hadith:

Follow up between Hajj and Umrah (i.e. continually repeat the
performance) because they both eliminate poverty and sins just like a
furnace eliminates the dirty impurities of iron, gold and silver. And
an accepted Hajj has no reward less than paradise! (Collected in Tirmidhi)

Also, there's the hadith about the fly:

The Prophet said "If a house fly falls in the drink of anyone of you,
he should dip it (in the drink), for one of its wings has a disease
and the other has the cure for the disease." (Collected in Bukhari)

Following any commands of rasulullah are counted as ibaadah (obviously). Here, he mentions dipping the fly in, for the benefit of nullifying the disease.

So again, sometimes we know, and sometimes we don't know, the reasons and benefits. We only need to submit; we can definitely investigate and find out if we are able to.